The story below quotes Whole Foods co-CEO John Mackey as saying the company ultimately plans to triple the number of stores to 1,000 and decrease the average store size to approximately 40,000 square feet.
According to the story, Whole Foods opened 16 stores in 2010 averaging 42,600 SF, and seven stores so far this year, averaging 40,000 SF. In addition, the 61 stores currently in development average just under 40,000 SF.

The Packer – Whole Foods targets smaller stores, more locations – Retail